Exposed export product flags in batch runner

extensions/chaeo/examples/batch_run_patches.py

@@ -9,7 +9,7 @@ from model_server.accessors import InMemoryDataAccessor, write_accessor_data_to_
 
 if __name__ == '__main__':
     where_czi = Path(
-        'c:/Users/rhodes/projects/proj0004-marine-photoactivation/data/exp0038/AutoMic/20230906-163415/Selection'
+        'z:/rhodes/projects/proj0004-marine-photoactivation/data/exp0038/AutoMic/20230906-163415/Selection'
     )
 
     where_output_root = Path(
@@ -54,6 +54,13 @@ if __name__ == '__main__':
             'mask_type': 'boxes',
             'zmask_filters': {'area': (1e3, 1e8)},
             'zmask_expand_box_by': (128, 3),
+            'export_pixel_probabilities': False,
+            'export_2d_patches_for_training': True,
+            'export_2d_patches_for_annotation': False,
+            'export_3d_patches': False,
+            'export_annotated_zstack': False,
+            'export_patch_masks': False,
+            'export_patch_label_maps': True,
         }
 
         result = export_patches_from_multichannel_zstack(**export_kwargs)
@@ -61,7 +68,7 @@ if __name__ == '__main__':
         # parse and record results
         df = result['dataframe']
         df['source_path'] = ff
-        df.to_csv(where_output / 'df_objects.csv', **csv_args)
+        df.to_csv(where_output / 'df_objects.csv', index=False, **csv_args)
         pd.DataFrame(result['timer_results'], index=[0]).to_csv(where_output / 'timer_results.csv', **csv_args)
         pd.json_normalize(export_kwargs).to_csv(where_output / 'workflow_params.csv', **csv_args)
         csv_args = {'mode': 'a', 'header': False} # append to CSV from here on

extensions/chaeo/workflows.py

@@ -24,10 +24,12 @@ def export_patches_from_multichannel_zstack(
         zmask_filters: Dict = None,
         zmask_expand_box_by: int = None,
         export_pixel_probabilities=True,
-        export_2d_patches=True,
+        export_2d_patches_for_training=True,
+        export_2d_patches_for_annotation=True,
         export_3d_patches=True,
         export_annotated_zstack=True,
         export_patch_masks=True,
+        export_patch_label_maps=True,
 ) -> Dict:
 
     ti = Timer()
@@ -81,7 +83,7 @@ def export_patches_from_multichannel_zstack(
         )
         ti.click('export_3d_patches')
 
-    if export_2d_patches:
+    if export_2d_patches_for_annotation:
         files = export_multichannel_patches_from_zstack(
             Path(where_output) / '2d_patches',
             stack,